Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= TCDB::Q88P35 (384 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 205 bits (521), Expect = 2e-57 Identities = 128/311 (41%), Positives = 176/311 (56%), Gaps = 21/311 (6%) Query: 3 TLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGGAI 62 T+ +R+V K +G L + L I DGE L L+GPSG GK+TL+ IAGLE G + Sbjct: 2 TIAIRSVEKQFGRY--PALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQV 59 Query: 63 LIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVAR---- 118 L D QDV+ S R + VFQ YAL+ M+V +NI FGL +RK E+AR Sbjct: 60 LFDGQDVTYASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEE 119 Query: 119 VAKLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEM 178 + KL+++E L R P+QLSGGQ+QRVA+ RALA +P + L DEP LDA +R +R E+ Sbjct: 120 LLKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRREL 179 Query: 179 KLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGS 238 + +H TT++VTHDQ EA+ L D+VA++ +G I+Q GTP Q+++ P FV F+G Sbjct: 180 RRVHDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFVG- 238 Query: 239 PPMNFIPVRLARQDGRLLALLDSGQARCELPLGEAADALEGREIILGIRPEQIALGAADG 298 R DG++ SG L A AL+ +RP AL A G Sbjct: 239 --------EANRFDGQV-----SGGRFKAGALTVPASALKDGAATAYVRPHDFALDEA-G 284 Query: 299 NGLPAIRAEVQ 309 + RA+VQ Sbjct: 285 FEVLIERAQVQ 295 Lambda K H 0.320 0.137 0.391 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 342 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 384 Length of database: 339 Length adjustment: 29 Effective length of query: 355 Effective length of database: 310 Effective search space: 110050 Effective search space used: 110050 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory